Comparative genomic analysis of nine Sphingobium strains: insights into their evolution and hexachlorocyclohexane (HCH) degradation pathways

Abstract

BackgroundSphingobium spp. are efficient degraders of a wide range of chlorinated and aromatic hydrocarbons. In particular, strains which harbour the lin pathway genes mediating the degradation of hexachlorocyclohexane (HCH) isomers are of interest due to the widespread persistence of this contaminant. Here, we examined the evolution and diversification of the lin pathway under the selective pressure of HCH, by comparing the draft genomes of six newly-sequenced Sphingobium spp. (strains LL03, DS20, IP26, HDIPO4, P25 and RL3) isolated from HCH dumpsites, with three existing genomes (S. indicum B90A, S. japonicum UT26S and Sphingobium sp. SYK6).ResultsEfficient HCH degraders phylogenetically clustered in a closely related group comprising of UT26S, B90A, HDIPO4 and IP26, where HDIPO4 and IP26 were classified as subspecies with ANI value >98%. Less than 10% of the total gene content was shared among all nine strains, but among the eight HCH-associated strains, that is all except SYK6, the shared gene content jumped to nearly 25%. Genes associated with nitrogen stress response and two-component systems were found to be enriched. The strains also housed many xenobiotic degradation pathways other than HCH, despite the absence of these xenobiotics from isolation sources. Additionally, these strains, although non-motile, but posses flagellar assembly genes. While strains HDIPO4 and IP26 contained the complete set of lin genes, DS20 was entirely devoid of lin genes (except linKLMN) whereas, LL03, P25 and RL3 were identified as lin deficient strains, as they housed incomplete lin pathways. Further, in HDIPO4, linA was found as a hybrid of two natural variants i.e., linA1 and linA2 known for their different enantioselectivity.ConclusionThe bacteria isolated from HCH dumpsites provide a natural testing ground to study variations in the lin system and their effects on degradation efficacy. Further, the diversity in the lin gene sequences and copy number, their arrangement with respect to IS6100 and evidence for potential plasmid content elucidate possible evolutionary acquisition mechanisms for this pathway. This study further opens the horizon for selection of bacterial strains for inclusion in an HCH bioremediation consortium and suggests that HDIPO4, IP26 and B90A would be appropriate candidates for inclusion.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-1014) contains supplementary material, which is available to authorized users.

Comparison of the complete genome sequences of four γ-hexachlorocyclohexane-degrading bacterial strains: insights into the evolution of bacteria able to degrade a recalcitrant man-made pesticide

“…1) and genome organization have been intensively studied 16–19 . Recently, many draft genome sequences of other HCH (including not only γ-HCH but also other HCH isomers) degraders and their related but non-HCH-degrading strains were determined, and their comparative analyses have been published 20 , 21 . These studies provided us some important primary information on the evolution of HCH-degraders with the involvement of plasmids and insertion sequences (ISs).…”

Metabolic pathway and cell adaptation mechanisms revealed through genomic, proteomic and transcription analysis of a Sphingomonas haloaromaticamans strain degrading ortho-phenylphenol

“…Variation in the size and the GC content of the genomes of Sphingomonads has been attributed to the presence of plasmids and genomic islands 18 . A total of 4630 ORFs were predicted.…”

Evolutionary Genomics of an Ancient Prophage of the Order Sphingomonadales

“…Whereas none of the ORFs from region III had orthologs among other Sphingomonas spp., at least five ORFs from region II had orthologs among members of the same genus. Furthermore, almost all ORFs from region III had orthologs in Sphingobium ummariense RL-3, which was a hexachlorocyclohexane-degrading bacterium isolated from soil in northern India (Singh and Lal 2009; Verma et al. 2014).…”

“…These studies have also documented the occurrence of putative genes encoding oxygenases and glycoside hydrolases, which could facilitate survival in a variety of niches and the degradation of pollutants (Aylward et al. 2013; Verma et al. 2014).…”